Bwasw rewrite

Adds missing RG headers and tags, more robust SAM fixer, better error
reporting.

Squashed commit of the following:

commit b9f7b8e3f9e3bb03bcda9be4eac9b38da160fefd
Author: Ian Ferguson <iferguso@genome.wustl.edu>
Date:   Tue Jun 4 13:27:45 2013 -0500

    Fix issue with headers in bwasw

commit bef593058693bcb3407a33dd6a9cf2e14d34cedc
Author: Ian Ferguson <iferguso@genome.wustl.edu>
Date:   Wed May 29 15:39:17 2013 -0500

    Clean up Bwasw _run_aligner, better header handling

commit bfc6d676f1c1a08746cde9c6a8dc63dec1187048
Author: Ian Ferguson <iferguso@genome.wustl.edu>
Date:   Thu May 23 15:34:40 2013 -0500

    More Bwasw fixes, testing in pipeline

commit 31d3fe0293cc19358788d011eab18480beeaeeb5
Author: Ian Ferguson <iferguso@genome.wustl.edu>
Date:   Wed May 22 14:13:39 2013 -0500

    Manually merge in rusage changes

commit a3f769482940e4a3eca0e880ca989128b62a4135
Author: Ian Ferguson <iferguso@genome.wustl.edu>
Date:   Wed May 22 12:27:31 2013 -0500

    Bwasw aligner module development

    Work in progress: adding RG, refactoring sam fixer